Circulation of pathogenic and multidrug resistant Escherichia coli in animals

大肠杆菌是肠道微生物区系中常见的细菌，包括各种不同的克隆，从导致动物严重疾病的高致病性大肠杆菌到非致病性共生大肠杆菌。在致病性和共生性大肠杆菌分离株中发现了很高的抗菌素耐药性。目前，养猪业和家禽业都处于十字路口，几乎没有其他方法来治疗由此导致的几乎流行的大肠杆菌感染。然而，关于这些菌株如何能够成功地出现和传播，以及哪些细菌或其他因素可能会影响这一点，人们知之甚少。 本研究计划的总体目标是调查耐药和致病性大肠杆菌在养殖场猪和家禽中的时空传播情况，并确定影响这种传播的危险因素。我们正在使用两种模式来帮助实现这一目标。1-家禽业在孵化前对所有雏鸡停止系统地给予抗菌剂；2-高致病性和广泛抗药性的大肠杆菌菌株在断奶后使用预防性抗菌药物的猪中的出现和流行传播。 在这两个模型中，将使用类似的方法来表征大肠杆菌分离株，以研究新的广泛耐药克隆的出现或消失的机制，以及克隆和质粒在抗菌素耐药性和毒力传播中的相对作用。在全基因组测序和更完整的克隆分析之后，将通过全基因组系统发育方法筛选分离株的毒力和抗药性基因图谱。 这项研究的一个新颖方面是，我们有使用真实情况的第一手模型，在这种情况下，细菌毒力和多药耐药性一起创造了一种危机情况。这项研究将提高我们对高危克隆如何出现、传播并有助于增加抗菌素耐药性传播的知识。它将阐明如何“管理”生产动物，以便将抗菌素耐药性的传播减少到可接受的水平，允许继续明智地使用关键抗菌剂，并减少抗菌素耐药性决定因素向人类传播的风险。

Escherichia coli are common bacteria in the intestinal microbiota, and include a broad variety of different clones, ranging from highly pathogenic E. coli causing severe disease in animals to non-pathogenic commensal E. coli. A high prevalence of antimicrobial resistance has been found in pathogenic and commensal E. coli isolates. Presently, both the pig and poultry industries are at a crossroad, with few alternatives for treatment of the resulting almost epidemic E. coli infections. However, little is known of how these strains are able to succeed in emerging and spreading and what bacterial or other factors may influence this. The overall goal of this research program is to investigate the spatio-temporal spread of antimicrobial resistant and pathogenic E. coli in pigs and poultry on-farm and to identify risk factors influencing this spread. We are using two models to help achieve this goal. 1- Withdrawal by the poultry industry of systematic administration of an antimicrobial to all chicks prior to hatching and 2-Emergence and epidemic spread of highly pathogenic and extensively drug resistant E. coli strains in pigs where preventive antimicrobial medication is used after weaning. In both models, a similar approach will be used for the characterization of E. coli isolates in order to investigate the mechanisms of emergence or disappearance of new extensively drug resistant clones and the relative role of clones and plasmids in the spread of antimicrobial resistance and virulence. The E. coli virulence and antimicrobial resistance gene profiles of isolates will be screened following whole genome sequencing and a more complete clonal analysis by whole genome phylogenetic approaches. A novel aspect of this research is that we have first-hand models using a real situation in which bacterial virulence and multidrug resistance are coming together to create a crisis situation. This research will improve our knowledge of how high-risk clones can emerge, circulate, and contribute to increasing the spread of antimicrobial resistance. It will shed some light on how to «manage» production animals in order to reduce the spread of antimicrobial resistance to acceptable levels, allowing the continued judicious use of key antimicrobials and reducing the risk of transmission of antimicrobial resistance determinants to humans.